Microextractors are known to provide high mass transfer rates for the extraction and separation of rare-earth elements (REEs). High-throughput microextractors are essential for industrial-scale production of REEs, but few practical studies have been conducted to date. In this work, a chaotic advection microextractor, i.e., a three-stage microextractor, was designed and demonstrated to extract Pr(III) and Ce(III) efficiently from nitric acid media at high throughputs by using 2-ethylhexyl phosphoric acid-2-ethylhexyl ester (P507) and sulfonated kerosene as an extraction agent and a diluent, respectively. Flow visualization experiments showed that the dispersed phase could be effectively broken into small droplets owing to vortex and recirculation flows. Microextraction experiments performed under optimal extraction conditions indicated that at low throughputs, the concentration ratio D, extraction efficiency E, and separation factor beta decreased with an increase in the throughput, whereas at high throughputs, D, E, and beta increased with an increase in the throughput. An extraction efficiency close to that of co-current balanced extraction was successfully achieved, even at a high total throughput of 100 mL/min and a rather short residence time of 0.029 s. Thus, the chaotic advection microextractor features a high throughput and high extraction efficiency, which are appropriate for the high-efficiency extraction and separation of REEs.